PESHAWAR — While Americans are focused on the U.S. fight against the Taliban in Afghanistan, an equally critical battle is being waged by the Pakistani army against Taliban groups next door.

The need for U.S.-Pakistani military cooperation in the struggle against militants has never been greater. Yet America’s relationship with Pakistan and its army is so clouded by mistrust that full cooperation cannot happen.

That gap is something neither side can afford. It undercuts NATO efforts to stabilize Afghanistan and harms Pakistani efforts to crush the jihadis who have become an existential threat to their state.

Most Americans know that al-Qaeda’s leadership, and key Afghan Taliban leaders, are thought to be hiding in the mountainous areas of Pakistan along the Afghan border. But fewer know that the Pakistani military launched several major campaigns against some of the country’s own Taliban groups, after failed efforts to cut peace deals. A serious effort to clear a nasty group known as TTK (Tehreek-e-Taliban) out of South Waziristan is going on now.

In retaliation, TTK has launched a wave of suicide bomb attacks that have turned the regional capital of Peshawar into a mini-Baghdad, circa 2005. Pakistani TV screens are filled with scenes of carnage; a week ago bombers hit twice, once attacking a court building (civilian legal institutions are a target). People are staying off the streets, and many downtown offices are moving employees to safer locations.

Meantime, Islamabad’s roads are laced with checkpoints; blast barriers have gone up around big hotels and United Nations offices. Since my last visit in April, even military offices in Rawalpindi are more heavily barricaded, after the general headquarters was recently attacked.

Yet you’d be hard pressed to get the sense that Pakistanis and Americans are fighting on the same side. Rampant anti-Americanism among ordinary Pakistanis spawns bizarre conspiracy theories. One typical fantasy: A retired Pakistani general, Mirza Aslam Beg, claims that U.S. military helicopters spirited the top TTK leadership across the border to safety in Afghanistan.

Although the Pakistani military and ISI intelligence service now appear committed to fighting Pakistani Taliban groups, analysts here say some officers are still conflicted about whether the army should be battling other Pakistanis. “They say all this is being orchestrated by America to create instability in Pakistan so they can steal our nukes,” says a well-known nuclear physicist and political analyst, Pervez Hoodbhoy, who opposes such perverse thinking. But this popular theory can be heard from many well-educated people in Islamabad.

The U.S. and Pakistani militaries have well-known grievances against each other. Among them: Pakistanis think the United States made a mess in Afghanistan that has fed militancy in their country. U.S. officials think the Pakistanis are protecting Afghan Taliban leaders, some of whom the Pakistanis trained, because they believe the Taliban may one day return to power in Kabul and provide Pakistan with an ally against India, a claim Pakistani brass reject.

What is clear, however, is that each military could use more help from its counterpart. Pakistan’s struggle against its militants is only beginning.

The Pakistani military wants more U.S. help — and pressure on the Afghan government — to try to seal the border so Pakistani jihadis cannot escape, and Afghan jihadis enter. Moreover, say analysts here, the Pakistani army wants any U.S. drone attacks to target the Taliban leaders they are fighting in South Waziristan, and not hit others whom it doesn’t see as an internal threat.

But the White House wants Pakistan to expand the attacks to target Pakistani locales where Afghan Taliban, such as Mullah Omar, are supposedly hiding. President Obama’s national security adviser, James Jones, just visited Islamabad and delivered this message. “Our response to Mr. Jones,” Pakistan’s military spokesman, Gen. Athar Abbas, told me, “is that we do not have unlimited resources.”

In other words, each side is focused on the particular Taliban groups that it sees as a security danger. Yet these groups are so interlinked that it’s hard to see how they can be checked without a joint effort.

There are some signs of progress. U.S. officials say that U.S.-Pakistani military cooperation is on the upswing (former TTK leader Baitullah Masood was taken out by a U.S. Predator drone.) Abbas pointed out that “NATO provided an anvil” from the Afghan side of the border when Pakistani troops were fighting militants in the tribal area of Bajaur.

Pakistan’s army needs more help with equipment; its civilian government needs funds and prodding to reconstruct tribal areas cleared of militants, so the population won’t welcome them back. The United States can help with both. Pakistani military and intelligence agencies may be reluctant to take on Afghan Taliban leaders on their soil, but they could help mediate a political solution in Afghanistan.

Yet the gap in perceptions is so wide, the suspicion of U.S. intentions so ingrained, that it’s hard to imagine the trust deficit being bridged in the short term. “What is truly needed is to look at it as a regional problem and cooperate at the highest level,” says retired Lt. Gen. Talaat Masood. Until that happens, it will be hard for either side’s fight against the Taliban to succeed.

Trudy Rubin is a columnist and editorial board member for the Philadelphia Inquirer, Her e-mail address is trubin@phillynews.com.

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